Shadows
by SweetMint9
Summary: "Shadows are a ninjas best friend... but sometimes they can betray you..." Raphael keeps having nightmares, when he decides to take a walk in the sewers one night he discovers never to mess with shadows. Rated T for some language, and violence . Disclaimer: I do not own TMNT...
1. Nightmares

_**Hey! SweetMint9 here! I wrote a new story! This one is more sad, hope you like!**_

* * *

When Shadows Attack

"NOO!" Raphael yelled at the top of his lungs at the sight of his brothers laying on the floor lifeless, tears started forming as he looked around looking for the murderer rage starting to form in him, he spotted some shadows moving, he threw his sais at them aimlessly.

"You did this Raphael…" A voice coming from the shadows said "Do not blame me for your weakness" it said before the shadows faded away.

Raphael let out a scream of agony as he rushed to his brothers, his hands were covered in blood from his brothers, but he didn't care, he fell to the floor and started crying, why were these things happening to him? He asked himself over and over again. He stood up and walked to the edge of the building, he looked down, it was at least 5 stories tall, he looked up at the night sky and wiped a stray tear away.

"I'll see you soon brothers" He said before jumping down and landing on the cold concrete floor…

Raphael woke up panting from the nightmare he just had, it wasn't the first time this happened to him, he had been having this nightmare for weeks now, but still couldn't get over it. He choke a sigh realizing it had only been a nightmare, he set his head down on his pillow and looked over to his clock, it was nearly 3 a.m. He decided it was no use going to sleep now, even though he usually woke up 2 to 3 hours later, he got up from his bed and headed out the door, being as quietly as he could not wanting to wake up his brothers and sensei, he hurried out of the lair walking thru the labyrinth of tunnels that composed the sewers of NYC. Having done this before he wasn't worried about having to deal with his sensei about leaving the lair at night. He got to a certain part of the sewers where he didn't know about yet.

"I don't remember this place…" Raph said before entering the unknown tunnel. He walked for a while listening to his surroundings and using all his ninja senses, there was absolutely no sound at all, nothing but the light sound of his footsteps and breathing. "Ugh! The silence is killing me" Raph thought to himself and decided to return home when he saw a dim light in the distance. "Huh?" He started walking towards it, the closer he got the brighter it became, but when he came even closer the bright light suddenly turned off and became a dark blue-ish before darkness surrounded the mutant turtle. "What the-" Raph said as he felt something pull at his feet, having no time to react he was only able to let out a yell before being pulled down into the ground.}

_TBC…_

* * *

**_Yea It´s short but I will upload the next chapter as soon as possible. Thanks for reading!  
_**


	2. The Curse

**Hey guys! Here´s chapter 2! Enjoy, fav. follow, review or just read, whatever you wish to do! :D**

* * *

When Shadows Attack Ch. 2

The Curse

Raphael couldn't see anything, everything was pitch black, his heart was beating fast and he was silent. He could hear whispers and murmurs also the sound of something being dragged against a concrete floor. He placed his hands on his sais ready to attack whoever was there.

There was a moment where all the whispering sounds died off and there was a long silence where nothing but the sound of Raphs breathing could be heard, suddenly someone or something turned on a light switch, Raph was in a part of the sewers he didn't know about and there was no one with him, he picked his sais and twirled them looking around at his surroundings, nothing, there was nothing, nothing but shadows and the brick walls.

"Come out! " Raph yelled "I know you´re out there!"

Raph took a few steps forward, he then felt something or someone strangling him, he couldn't see who it was; he tried striking whoever it was with his sai, but with no effect. He then fell to his knees after the sensation of someone strangling him continued, he started to black out until that sensation suddenly stopped, he then heard a light chuckle coming from the shadows.

"So… you are the one who dared trespass our part of the sewers" A female voice said to him.

Raph grunted and tried attacking. The voice only chuckled once more at him.

"Temperamental, huh? I think I could use that in my advantage." It said again.

Raph could feel his temper rising, he growled, "If you think I´ll ever be working for you then you are wrong!" he tried to strike at to where the voice was coming from with no effect. The voice chuckled at him again only more higher making sure he was getting angry.

This was going in for a while more, Raph was getting more tired by the minute, he was breathing heavily and was even having trouble to stay up, until, finally, he collapsed on the floor out of tiredness. The figure chuckled once more.

"Now, it is our chance" It said coming out of the shadows, it was a cobra like creature with dark purple skin with dark blue patterns with silver eyes. "Keira! Now is your chance…"

Behind her appeared another cobra like creature but smaller with almost the same patterns but with amber eyes.

"I´m not sure if I can do this mother" she said shyly

"You will do as told!" The mother snapped in return and pushed her daughter forward.

Keira shut her eyes and concentrated everything around her moving slightly, she then came forwards to Raphael.

"Ugh.." Raph groaned and hold his throbbing head, he looked around , everything was dark, a voice started speaking to him.

"Raphael…" The voice said "so that is your name"

Raph grunted once more, "Who are you!"

"My name is Keira, the daughter of the shadow queen, which means I´m the princess" Keira said appearing in front of him.

"Get out of here! What are you doing in my head!?" Raph yelled.

"I´m sorry… but it´s my mother's orders" she said before a dark purplish ring appeared around her and attacked Raph.

_TBC..._


	3. The Deal

Raphael screamed in his sleep, he was having a terrible headache, he felt as if his head was going to explode. Suddenly, he opened his eyes and stood up, so did Keira.

Raphs eyes changed to a golden brown color, and appeared to have his energy back.

"You are under my control now" Keira said, her mother smiled proudly.

"Under OUR control Keira" She said, Raphael slowly nodded, clearly under control.

* * *

Leonardo woke up from his slumber, he yawned and stretched, he got out of his bed and headed outside, he knocked on his brother's doors.

"Come on guys! Wake up!" Leo said, Donatello and Michelangelo walked out their rooms. Raphael was still missing.

Leo knocked on his door again, after receiving no response he barged in.

"Raph! Wake up!" Leo said before noticing his brother was not in his room. They searched for him but he was nowhere to be found. Leo started to worry. They walked to the dojo where Splinter was waiting for them.

"Sensei! Raph is missing!"

* * *

Raph was lying on the floor in a dark room, he looked beaten up. He weakly opened his eyes and stood up.

"Where am I?" He said to himself.

"Inside your mind dear" A female voice responded, he looked to where the voice came from, he saw Keira.

"You?! Get out of my head!" He said to weak to walk towards her.

"I was thinking that I at least told you what the deal is" she said coming closer.

"Deal? What deal?"

Keira looked as if she was concentrating once again, an image appeared in front of them, it showed the city, then Raphael running and jumping across rooftops, he stopped at the entrance of a jewelry store.

"T-that's me!?"

Keira nodded. The scene kept playing as if it were a movie.

Raphael then broke the windows and the alarm sounded, he grabbed some jewelry with a dark looking gem.

"W-what am I doing!?" Raph said "I don't steal!" He looked to Keira.

"You are doing this! Stop it!" He tried charging but was still too weak and fell down.

"I'm sorry, but as I said, it is my mother's orders" she said "My mother and her subjects need these gems, they hold great power, but the humans only see them as gems, to keep our kind living we need these gems"

"Why the hell do you need me for?" Raph said "Since you can disappear"

"We cannot risk being seen" Keira said, "I will now stop controlling your mind" she closed her eyes for a moment and opened them quickly.

* * *

Leonardo, Michelangelo and Donatello walked by the sewers the sound of water rushing in the distance and small furry creatures running around were the only sounds heard, no one made a sound, not even Mikey.

"You don't think he went that far off right?" Donnie dared speak up.

"He better have not" Leo muttered "Is he anywhere near?"

"The signal of Raphs T-phone shows that he went that direction"

They all ran towards that direction and came to a dead end, no one was there.

* * *

Raphael woke gasping for air, he looked around, he was still in the same dreaded room he was when he was knocked unconscious. A shadowy figure emerged from the darkness smirking at him.

"Good job Keira" she said and ordered some of her subjects to retrieve the gems.

"I might as well present myself" She said stepping out of the shadows "I am Kali, the shadow queen, you must be Raphael, it always pleases me to have a new servant" she said with a smirk. Raph growled.

"I am NOT your 'servant'" He said with gritted teeth "Nor will I ever be especially to someone like _you_!"

Kali hissed at him but calmed down a bit.

"Well then, I guess you don't want to see your brothers ever again"

Raph let out a small, but audible, gasp. He then growled again.

"Don't you DARE, hurt my brothers!"

She smirked.

"I guess, we have a deal then…"

_TBC…_


	4. Mistakes

**Hello, sorry for the long wait, but anyways I bring you a new chapter. BTW, I changed the title a little. Warning: There is some strong language in this chapter.**

* * *

Shadows Ch. 4

Mistakes

Leonardo, Donatello and Michelangelo stood in front of the dead end of the tunnel all of them feeling both shocked and worried about their missing brother.

"I-I don't understand!" Donnie stammered "The signal leads to here!"

"Then where is he?" Leo said.

"Guys…" Mikey said taking a few steps forward and picking up something from the sewer floor; it was Raphs T-phone.

* * *

Kali chuckled and smirked at Raphael.

"I guess we have a deal then"

"Only, if you leave my brothers out of this!"

"Oh, of course I wouldn't want to hurt your precious little brothers now would I?"

Raph growled. Kali smirked once more.

"Well then!" She turned to her daughter "Keira! Take our…guest… to his home, we wouldn't like him to die in the cold sewers would we?"

Keira just nodded and once again began to control Raphael's mind, Raphael yelled again while he clutched his head, then it stopped and once again his eyes turned into a golden brown color, signaling that he was under control.

* * *

"Ugh!" Raphael moaned as he woke up, the room was dark except for the cobra like creature that stood a few feet away from him with her eyes closed concentrated on something. Raphael took the opportunity and slowly and stealthily stood up and began walking towards her; slowly he took out his sais and swung at her head. But before they made contact she disappeared in a dark cloud of smoke and appeared behind him.

"I must warn you to not do that" She said as she knocked Raphael forwards "We do not like traitors and my mother knows how to deal with them when she finds one"

Raphael just growled.

"You're lucky I'm not my mother"

"Can you get out of my head already?" Raph yelled "I'm sick of it! Now where are you taking me?"

"To your home dear" She said once again closing her eyes. "By the way I must warn you that you will not tell anyone about us, unless, you want the people you told our secret to be in the same situation as you"

Raph glared at her but said nothing; he just waited until they got home.

* * *

Raphael woke gasping for air and looked around, he found himself in his room, away from any shadow creatures that threatened to take over his mind. It had all been a nightmare… or so he thought…

He got up and walked out of his room, he looked around and saw no one, he headed to the living room where his three brothers were. He cleared his throat for them to acknowledge his presence. Three pairs of eyes looked at the source of the sound and jumped up from the couch.

"Raph!"

Raphael felt someone squeeze him tight he looked down, it was Mikey.

"Raph! We were so worried!" Michelangelo said still hugging him tight.

"Where were you?" Leonardo said "You know you are not allowed to go out of the lair to late at night"

"I only went for a short walk" Raphael argued "No big deal!"

"No big deal?!" Leo shouted "We found your T-phone in a restricted part of the sewers Raph!"

Raphael glared at him "Look, let's just forget about this ok? I'm fine so there's nothing to worry about" He got on the couch and turned on the television trying to avoid a fight, which was not a normal thing for him to do.

Leo glared at him but said nothing and sat next to him watching Raphael skid through channels until he decided to watch a wrestling match, they watched it in silence but a few minutes later the program was interrupted to show breaking news.

"_Jewelry stores have been robbed all around NYC"_

Raphael's heart stopped for a moment and he tried to change the channel but Leo stopped hm.

"No, wait I want to see this" He said and took the remote out of his hands.

"_The only clue we have about the culprit is in the following video"_

A video from a security camera appeared, its contents showed someone breaking in and stealing some jewelry and very quickly escaping.

"Wait, rewind the video back a bit" Donatello said who was also watching, Leonardo rewinded the video. "There! Stop!"

Leonardo paused the video, a glimpse of green skin and a shell was on the video, he felt rage, already knowing who it was, he stood up angrily and faced his younger brother.

"Raphael, you- you were _stealing_?! How could you!" Leonardo shouted angrily.

Raphael was not fond at being yelled at, and he always fought back, and this was no exception.

"I wasn't stealing Leo!" Raph yelled back "I-"

"You what?" Leo responded "Who else could be the one in the video, huh?"

Raphael growled.

"What will father say about this huh?" Leo kept yelling "He will be greatly disappointed in you!"

Raphael felt himself getting angry very quickly.

"Besides stealing you put us in danger Raphael! You were clearly visible in the damn video! What if someone tracked you back into the lair! Is that what you want? To put us in danger?"

Raphael was furious with Leonardo's accusations.

"Shut it Leo!" He said through gritted teeth.

"No! You will be hearing this from me and from Splinter once I tell him for so much time!" Leo said "I might as well go tell him! I can't wait to hear what he has to say about you being a dumb-ass!"

Raphael saw red, he grabbed one of his sais and sliced it across Leo's face, he could have continued, but Leo's pained cry brought him back to earth, once realizing what he had done he dropped his sai on the floor and backed away, the sight of his brother was horrible to him, Leo's face had blood coming from his forehead to his cheek, puddles of blood had already began forming under him, and were covering his arms and legs. Donatello and Michelangelo immediately went to his aid, Splinter coming in from the dojo only milliseconds later. Everyone looked at Raphael with shocked, angry and disappointment on their faces. _Disapointment._

"Raphael…" Splinter calmly tried to reach out to him.

Raphael shook his head slowly in fear before backing up and darting away from the lair.

* * *

**Well, this is my longest chapter update 'till now, hope you liked.**


	5. New Recruit

Shadows Ch. 5

New Recruit

Raphael ran out of the lair and kept running aimlessly tunnel after tunnel until his lungs couldn't take no more and he collapsed to his knees and began to sob in his hands. He had hurt his brother, instead of protecting him which was why he let the shadow queen and princess control his mind, to protect his brothers and now he had hurt one of them, and his brothers would never forgive him.

He continued quietly sobbing in his hands. What had he done? Why did he had to lose his temper? He had never, not even when they were children; hurt that badly one of his brothers because of his temper.

"Why am I so stupid?!" Raphael mumbled to himself.

"Hmm, I knew you had a temper…" A voice said, Raphael looked up, it was Keira. "But I didn't know it was that bad"

Raph tried to wipe away the tears, but were being quickly replaced with new ones.

"G-go away K-Keira!" Raph said.

She shook her head. "Look, I may look like a heartless witch, but I am not, ok?"

Raphael just stared at her.

"That is one thing I am different from my mother, and I can assure you I'm nothing like her"

Raphael still remained silent.

"Follow me, I know a place where you can stay." she said slithering past him.

Raphael hesitated but followed eventually.

"Keep still Leo!" Donatello said trying to clean Leonardo's wound.

"I must find Raph!" Leo said "This was my fault."

"What? Of course not Leo"

"It is! If I wasn't raging at him and just let it cool down, this wouldn't have happened!"

"But Leo, you had every right to be mad at him, what he did was wrong"

Leo sighed and sat still.

"How bad is it?"

"Not too bad but it will need some stitches, you are lucky he didn't slash your eyes"

Leo sighed again "Yeah…"

The lab doors opened and Mikey came in with a concerned look on his face.

"How's Leo?"

"He will be fine Mikey, the wound isn't too serious."

Mikey sighed in relief

"So, about Raph…"

"What about him?" Leo responded wincing when the cold cloth touched his wound.

"Well he did slash at your face Leo, sensei hasn't come out of his room since the incident happened, I guess he's worried."

Leo sighed, "We will look for Raph once I'm done here"

Mikey nodded and walked out of the lab.

"What is this place?"

Raphael asked Keira once reaching their destination.

"It was once a subway station, but it was abandoned when a terrorist attack occurred, almost no one knows this place anymore" Keira said "You may stay here as long as you need, unless, you prefer to stay at my mother's dungeon. Oh, by the way, my mother would like to speak to you in a few hours; I will be here when that time comes"

Raphael just slightly nodded and said nothing watching her leave. The place was nice; it was a little smaller than the lair and had a few pieces of debris here and there, but other that it was ok. He sat down on the small sofa and decided to take a much needed rest. No wonder what Kali needed him for, and knowing her it's most likely nothing good.

"Here he is mother" Keira said bringing Raphael to her mother, Kali.

"Very well Keira, you may leave now, I wish to speak to him"

Keira slightly bowed before leaving. Kali chuckled at Raphael.

"So Raphael, I must say that little act of yours was rather… entertaining…" she smiled as Raph growled at her.

"I found a new recruit, he will be under your command" She said. "Bring Joshua!"

Raphael stared at the darkness for a moment until two shadow guards came in with a human boy no older than 13 years old. The boy was startled by Raphael's appearance. Kali chuckled.

"You will be responsible of watching over this child when you go "gem hunting". He may prove useful to you"

"Stay away from me you sick witch! I'm not a robber! So shut the fu-…"

The kid was cut short and let out a pained cry before stopping, his teal eyes were now silver, Kali was controlling him. She chuckled and clicked her tongue.

"Such a defiant child" She said "That will need to go away"

The boy nodded slowly in control.

"Well then, now both of you go and retrieve more gems"

"I'm not a babysitter Kali!" Raph growled at her. She shook her head and smirked.

"You just won't learn will you? Keira! You have work to do!"

Keira appeared seconds later and mouthed an "I'm sorry" to Raphael, knowing what to do she concentrated for a moment and Raphael let out a pained cry as well before falling silent once more.

Raphael was once again in the dark room of his mind with Keira a few feet from him, concentrated. He stood up and walked to her.

"So now where am I going?"

"To a jewelry store in central park, one of the biggest in NYC, and one of the most secure, that's why we needed two people for this job, the authorities would arrive before you could collect all the gems we need"

Raphael slightly nodded and let Keira do her job, even though he didn't like it, but there was no use in fighting, they were too powerful. Raphael could only sit and watch the scene of himself and this kid Joshua rob and leave the jewelry store quickly and escaping into the sewers where they finally had control of their minds again.

"Never do that again, bitch!" Joshua yelled at Kali who hissed and glared at hi in return.

"Shut it boy! I expect you to behave! I don't want to lose a new recruit so quickly."

The boy's glare died down and said nothing, she smirked at that.

"Very well then. Raphael will watch over you Joshua"

"I don't need a babysitter Kali! I can take care of myself!"

Kali laughed at that "You barely even now where the nearest manhole is! That is why Raphael here will be in charge of you, he knows the sewers well, both of you are dismissed" she said and faded away in the shadows. There was a short silence between the two for a moment. Raphael started walking towards his temporary hideout.

"Aren't ya coming?" Raph said and Joshua started following him. There was another silence on the way so Raph decided to speak up.

"So what brings you to the sewers?"

"Who? Me?" Joshua said surprised he spoke to him.

"No, the walls" Raph said sarcastically "Yes you! How did you get here?"

"I dunno my memory is kinda blurry" He said. "Why are you a giant talking turtle?"

"I dunno kid, destiny happened I guess"

Joshua just slightly nodded and continued walking towards Raphs temporary hideout. When they arrived Raph plopped down on the sofa and Joshua sat on a chair nearby.

"You have guts kid" Raph said all of a sudden "How you talked like that to Kali was pretty bad-ass"

Joshua chuckled and smiled. "I just have that in me"

Raphael returned the smile before drifting off to sleep.

_TBC…_


	6. Discoveries

**Hey people! Sorry for the long wait, I had writers block, but not anymore! So to compensate the long wait I bring you an extra long chapter! Enjoy!**

* * *

Shadows Ch.6

Discoveries

"Come on hurry up!" Leonardo said as they ran through the sewers. "We have to find Raph as soon as possible!"

"Leo, we have no idea where he went." Donnie said as he tried catching up with him. "He doesn't have his t-phone with him so we can't track him down"

"We will just have to search then, split up! We will find him faster that way!"

Each turtle ran a different direction.

* * *

Raph woke up with a start, another nightmare, possibly the third time that night. He sat up and looked around, a bit startled not recognizing at first the place he was in, but then realizing his nightmare was real, he was now pretty much a servant to Kali, the shadow queen, and Keira the shadow princess, and pretty much the whole shadow tribe, which is what they called themselves, he thought it was lame.

He looked at the young teen sleeping soundly on a small sofa; he was shifting a bit in his sleep.

"Must be having a nightmare" Raph thought.

"Good, you have awoken…"

Raph sighed, "What now Keira?"

"Mother wants me to tell both of you to come in half an hour; she wishes to speak with you both"

"We'll be there" Raph said, Keira nodded and turned to leave.

When she left Raph went to the still sleeping kid, he nudged him on the arm.

"Wake up kid"

A groan was the only response; Raph rolled his eyes and nudged him again.

"Come on kid"

Another groan, he then nudged him harder, Joshua woke up "What!?"

"Get up kid! Kali wants to see us."

He got up quietly and both got out of the small subway station. When they arrived Kali was there waiting for them.

"Good! You have arrived"

"What do you want Kali" Raph said.

"You will start to be trusted enough to go search for gems on your own, without one of us controlling your actions, but for that, you will start training your agility, speed and other things in case you come across a difficulty" She said "Come" She led them into a room filled with weapons and training dummies.

"Let's see how well you both are at this…"

_Two Weeks Later…_

Joshua slashed through a training dummy with a sword and quickly proceeded to slice down three more, Kali smirked watching them.

"Not bad kid" Raph said, Joshua smiled.

"Good, you may leave for now" Kali said dismissing them.

Joshua and Raph left the training room, but Raph stopped.

"Damn it! I left my sais back at the training room" Raph said "I'll be right back"

"I'll just head back to the lair"

Raph went back to the training room and saw Kali talking to Keira, they didn't seem to notice him.

"The newest two are doing very well" she said with a chuckle "Both have pure hearts, but that will be broken soon enough, slowly their hearts will become darker until they become into one of us, they will certainly be useful when they do" she laughed.

Raphael had heard everything, and backed up slowly and headed to his lair.

"How am I not surprised?" Raph mumbled to himself "I need to warn the kid that-"

"Do that and your brothers will be in a worse situation than you are right now" A voice said, it was Keira, Raph growled at her.

"I don't understand you, first you threaten me, than you try to help me and now you are threatening me again"

She shook her head "I'm trying to protect you-"

"I don't need protection" Raph said "I can take care of myself"

She shook her head again "No one deserves to fall into the hands of the shadow tribe"

"You say that?" Raph said "The daughter of the evil Shadow Queen"

She looked to the floor "You have secrets, so do I"

With that she slithered away, Raphael only watched her leave, curiosity gleaming in his emerald green eyes.

_One week later…_

"You will be trusted to retrieve the gems on your own, no controlling, but if you do something else, then we will be forced to make you do as we wish" Kali said to Raph and Joshua "Now go!"

The 'gem hunt' went pretty well, and was more organized than when the shadows controlled them. After that, Raphael walked to his lair pretty angry, Joshua followed him with a small smile and humming a tune.

"I can't believe I did that" Raph said.

"But we have stolen before, when they were controlling us"

"But this is different, this time we did it on our own will"

Joshua shrugged, Raph sighed.

_Two Weeks Later…_

After more robberies, security had increased greatly, but that didn't stop them, each night there would be a news article about the mystery criminals, and about a reward if they were caught, and so on.

Raph woke up and stood, he felt strangely empty and couldn't feel his feet, he looked down and saw his feet were slightly transparent and were turning an eerily shade of dark purple. Startled e woke up Joshua and saw that both were slowly turning into a shadow.

"What the hell!" Raph yelled

"Dude! This is awesome!" Joshua said.

"This is bad!" Raph yelled "Don't you see we are turning into one of them?!"

Joshua shrugged.

"_Slowly their hearts will become darker until they turn into one of us…"_

Raphael remembered Kali's words, Joshua seemed to not care about this whole situation, but why didn't he?

Keira appeared in their lair, she saw both of them but said nothing about it.

"Mother wants to see you"

"We'll be there in a moment" Raph said, Keira nodded and slithered away.

"We better get going" Raph said exiting the lair.

* * *

The rest of the turtles walked at a really slow pace into the lair, once again they had no luck in finding Raphael.

"Where could he be?" Leo said to no one in particular.

"He could be anywhere by now! He may have even left the city, if not the country!" Donnie said.

"I just want to find him" Mikey said a little teary eyed "I miss him…"

"We all do Michelangelo" Splinter said

"It is not like him to steal anything" Splinter said "Not even as a child he took something that was not his"

"Then there must be some thing or someone interfering, maybe the Shredder or the Kraang made Raph do that and he was trying to protect us" Donnie said thinking

"He would do anything to protect his family" Splinter said "What you said Donatello, could be true" Everyone shared a look.

"He may have not done this by choice…"

* * *

Raph and Joshua walked into the shadow queen's lair.

"We're here Kali" Raph said, looking around, she was nowhere to be found in the room. "Kali?"

With a cloud of smoke she appeared behind them.

They were startled, she laughed.

"What do you want?!" Raph growled, she calmed down and smiled.

"I just wanted to congratulate you, you did well"

"That's all?" Raph said she glared at him.

"…Yes, now, it seems the humans have finally figured out that you are only stealing one type of gem, they do not have any more in jewelry stores in the area of New York-"

"I'm not leaving New York!" Raph interrupted.

"Will you let me finish?!"Kali yelled. "There are many wealthy people in the rich part of New York, many known to have many of these gems in their possession" Kali continued "You will take these gems from them. That is all." With that she left in a cloud of smoke.

* * *

"Criminals looking for rare gems, HA!"

A man said to himself as he put his gems in a safe, entered a 5 digit combination and locked it.

"Let's see them get through this…" He mumbled to himself and left the room and activated his security system.

Mr. Richards was a wealthy msn, he knew many people and many more knew him, but he never told anyone about his possessions. How would these criminals know if he had any of those gems anyway? He told himself wondering if these people were dangerous, he wouldn't want to lose another member of his family as soon as he lost one already. He sighed, no; he would protect his wife, even at the cost of his own. He went to bed, his wife already asleep, he planted a kiss on her cheek, lay in bed next to her and drifted to sleep.

* * *

Sounds of alarms sounded in the home of Mr. Richards, he and his wife woke up startled, fear in their minds. He got up and grabbed the item that would inflict most harm closest to him, which happened to be a metal pole. He walked out of the room and told his wife to stay there. He quietly moved into the room, weapon at hand, the two criminals still there, though he couldn't see who they were only their silhouettes in the dark, one was trying to forcefully open the safe while the other looked out for cops.

"_God! How much are they going to take?!_" He thought referring to the cops.

One managed to open the lock and quickly grabbed the gems, they started to escape. He decided to take this into his own hands, with a battle cry he swung the weapon to the back of one, only to find out that it didn't hurt the criminal, it was like it had some sort of armor, he swung again only to be knocked down on his back.

"Go Raph! I'll keep him distracted!" One voice said, it sounded young, very young in fact.

One escaped and he decided to reach out for the light switch. Yes, he was very young indeed, even though he couldn't see his face, since it was hidden in a hoodie, but could see brown-golden hair and piercing electric blue eyes.

It couldn't be!

Could it?

He stared wide eyed.

"Joshua…?"

_TBC…_

* * *

**Oooh! Cliffhanger! Why do you think this man knows Joshua? Hmm? Stay tuned for the next chapter! :D**


	7. Secrets Revealed

**Oh my god! It has been forever since I updated this fic! I am so sorry! But here is the next (and really long) chapter!**

**... **

Shadows Ch. 7

"Secrets Revealed"

It couldn't be!

Could it?

Mr. Richards long lost son was standing right there in front of him glaring at him with icy electric blue eyes stealing his and his wife's jewelry.

He had to admit he felt hurt seeing his son stealing, but the shock of seeing him still alive surpassed that feeling. The boy didn't seem to recognize him. He dropped the metal pole and slowly approached him.

"Joshua…" he whispered, police sirens could be heard in the distance getting louder and louder as they approached but then the boy disappeared. He stood there shocked until the police and his wife came into the room.

"Honey, are you alright?!" she told him, he nodded slowly but said nothing, still lost in thought.

"Please tell me what happened." She told him quietly, he turned and looked at her.

"Joshua…"

She frowned.

"W-what about him?"

"He's alive…"

…

Kali smiled as her newest two brought her the dark looking gems and placed them in front of her.

"Excellent! You may go now." She said and ordered some other shadows to retrieve the gems. Raph and Joshua said nothing and turned to leave, they didn't speak on the way back to their old abandoned subway station but to say their "goodnights" and went to sleep.

…

Leo stabbed a Kraang droid in the back stealthily and watched as it fell to the ground making some kind of beeping noise and watched as the Kraang inside scurried away. They stayed in the shadows, they had no intention to fight the Kraang, they just came to see any clue about any of them holding Raph captive. Besides, there were too many Kraang for just the three of them to handle, they needed their brother back. They snuck into a room where according to Donnie was a Kraang computer, Donnie went to it and tried to hack into it to see if they had any information about Raphael. When he found nothing, he sighed and looked at Leo who was watching out for any Kraang.

"Nor the Kraang or the Foot Clan have Raph" he said sadly "Maybe he did do this on his own-"

"Donnie!" Leo cut him off having none of his little brother's pessimistic attitude. "Another villain could have him! You can't just give up that easily!"

"Sorry…"

Leo sighed "Let's get out of here and keep looking"

…

Raph woke up the next day, or night? He really didn't know anymore. He stood up and almost fell, he looked down and saw his legs were also becoming affected and turning a dark shade of purple, he growled. He needed answers. Before he could go find them Keira appeared behind him and startled him. He growled.

"I came to-"

"Kali wants to see us?"

"No, I sensed you wanted to ask something"

"Yes! What the hell is happening to us?!"

She sighed, and seemed to think for a while "Come with me if you really wish to know"

He followed her; they traveled around some dark and old sewer tunnels for some time until they entered an abandoned tunnel.

"What are we doing here" He asked her, barely able to see her in the dark, she having a dark skin color didn't help either.

"We are far away enough, the rest of the shadows can't enter our minds" she said and removed an old brick from the wall, sunlight entered immediately and illuminated the old tunnel, the light blinding Raph for a moment.

"Now, tell me what you wish to know"

"Like I said before; what is going on?"

"You are transforming, it happened to all of the shadows, were once human, some, even animal, the shadows entered their minds, controlling them and making them steal the gems we need, their hearts became obscure and obstinate, their minds making stealing a habit, something normal in their lives, until they transformed completely into a shadow, knowing pretty much nothing of their past" She said.

"I-is there a way to stop it? Or reverse it?"

"You cannot, as far as I now. There may be a way, but, who knows" she said "Anything else?"

"How did this all happen?"

She sighed "if you really wish to know, I'll start from the beginning, many years ago, an alien race from another dimension-"

"The Kraang?"

"Yes, they were making experiments on different reptilian species, they were messing with their DNA and adding chemicals, mutagen as they call it. That is when Kali was created, she was a mix of many different reptilian species, but now she had the power to control the minds of who she wants, she escaped the dimension in an inter-dimensional portal, and escaped into the sewers of this city. That is where I come in, I was once a human, a teenager to be exact I took a dare to enter the sewers from some friends, I wandered around until it was so dark and silent that I was afraid to move, that is where Kali found me, she threatened me to never go back to my family, or she would go after them, she used me to retrieve those gems, who the Kraang also created, the gems helped her stay alive, but she couldn't touch them directly, the were too powerful. Many weeks passed and more people were being victims of Kali, after a while I realized their hearts were becoming obscure, they were emotionless, we were all transforming, but only they were acting more like Kali. I don't know why I wasn't; I was the most skilled of all of them, Kali decided to take me in like her own daughter. She takes the mind of everyone who gets too close to our lair, the shadows can't go to the surface at day, sun light hurts them, that is another thing I'm different" she said admiring the light coming in the room, Raph listened closely.

"Do you think if she is defeated all of this will reverse?" He asked

"I do not know…" She replied honestly "Maybe, but I have never tried anything"

Raph sighed, he could try and defeat them and he could finally go back to his family, but, what if they were still mad at him? They were even happier without him, he sighed again.

"So, did Joshua come to close to your lair?" He asked

"No, Kali kidnapped him, and set up a false murder, she really needed more of those gems, and thought he was a good target"

Raph nodded slowly, a frown on his face.

"So, how many shadows are there till now?"

"2,327 to be exact" Keira said "Over the years numbers have increased greatly, you have no idea how many people wander around in the sewers"

Raph was shocked "That many? How old is this tribe?"

"More than 100 years old"

Raph was even more shocked "A-and how old are you?"

"82 years since Kali found me, in total about 96 years old, the transformation helped me not age as long as I'm in contact with the gems, technically, I'm still only a teenager" she smiled a bit at his shocked face.

"Anything else?" she asked him

"Why are you telling me this?"

"Because, I believe you are the one that can save us all, the one that is strong enough to defeat Kali, I see that in you, how it still bothers you to steal, how you still remember your family, how even though you think you have betrayed them, you still wish to go back. I see you have a good, strong heart, Raphael." She said. Silence was present for a moment, Raph thinking about what she had said.

Keira saw movement in the corner of her eye for a moment, her eyes widened slightly.

"We should return" she said and placed the old brick back into its place and led Raphael out of the tunnel.

...

"Ok, Donnie, you will keep a look out for Raph on topside, east and north side of the city. Mikey, you check west and south, I will search the sewers" Leo told them " take your T-phones with you, any signs of Raph or find yourself in any trouble call the rest immediately, now let's go!"

Everyone parted their ways.

…

A few hours later, Leo called Donnie and Mikey.

"Any sign of him?" He said as he kept walking around the sewers.

"No dude, I already checked the city twice but there is no sign of Raph" Mikey replied.

"Unfortunately no Leo" Donnie said "No sign of him topside anywhere"

Leo sighed; he approached the entrance of another tunnel, when he saw something out of the corner of his eye, a small red piece of fabric stuck in between some wood planks used to cover the entrance.

"Guys, I think I found something, come quick!"

…

Keira led Raph back to his lair.

"Thanks" Raph said

"My pleasure, I might return in a few hours, so rest for now"

Raph nodded and went back to his place on the couch.

'I must stop this transformation thing' Raph thought to himself 'I will not turn into one of them'

…

"Are you sure it was our son?" Mr. Richards's wife asked him

"I am positive" He said, she let out a breath.

"But everyone said he was murdered, I still can't believe he is dead"

"He is not dead, I saw him!" he said and sighed "he didn't seem to recognize me though, he was with someone else but I couldn't see who"

She sighed "Let's say he is still alive, why would he be stealing?"

"I do not know"

"The police searched for him around the city, but couldn't find him, they said they were going to give up the search.

He growled "Well if they aren't going to find them, then I will" he said and grabbed the metal pole he had earlier, he leaned in and kissed his wife "Take care, I will be back, and with our son"

…

"Look at this guys" Leo said as they went to the abandoned tunnel entrance he was earlier "Isn't this a piece of Raphs mask?"

"It could be Leo" Donnie said as he pulled out the fabric "I need to run some tests on it thought, it could just be some random piece of fabric that got stuck in between the wood"

"Ok, do what you have to do, but do it quick!"

…

"You will go to this mansion on Wall street, they have many gems in there, retrieve them all" Kali ordered to Raphael and Joshua who nodded and left.

They ran over the rooftops until they reached said mansion.

"Let's enter" Joshua said pointing at a chimney.

'If I keep doing this, I will transform' Raph thought.

"No" he said

"W-what?"

"You go, I will wait out here"

Joshua seemed hesitant, but shrugged it off and jumped in, Raph leaned against the back of the chimney.

'I hope this will work'

…

"No, no, no, no, no!" Kali said to herself "What is he doing!?" she growled "Keira!"

She appeared a few moments later.

"He is not cooperating!" She said "You know what to do"

Keira gave a small nod and began to concentrate.

…

Raph was still on the rooftop when his head started to hurt greatly, he held his head tightly and shut his eyes close and grunted in pain.

Once again, he appeared in his mind, Keira a few feet away as always.

"Forgive me for doing that" she said, he sighed.

"Why did you not listen to Kali?"

"I figured it would stop this transformation" he replied

"It could, but you are only risking your life"

"Better than turning into a shadow…" He said and waited for her to stop controlling him.

…

Raphael and Joshua walked into the shadows' lair and brought the gems they retrieved to Kali, after that they left.

Kali made sure they had left before angrily turning to Keira.

"Did you tell him?!" Kali yelled at Keira, who was startled by the outburst and looked confused.

"A-about what?" she said

Kali hissed at her "Don't be stupid!" she said narrowing her eyes "He is rebelling against us! He knows he can stop the transformation! And is strong enough to survive it!"

"I didn't tell him anything!" She said.

"Lies!" she yelled and took Keira by her neck strangling her "You know better than to betray me! I will let it slide this once but pull another stunt like that, and I will have your head!" she yelled empathizing the last part, with that she let her go and slithered away.

…

"Leo! I have the results!" Donnie said and Leo same right away.

"What did you find? Is it part of Raphs mask?"

"Definitely" he said "but there is something strange, not only has it have Raphs DNA but also something else's, a life form I have never seen before"

"Can you find out what it is? Maybe it has to do something to do with Raph"

"That's the thing Leo, after analyzing more about the other DNA I found something different in it"

"What?"

"Mutagen…"


End file.
